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  <div class="section" id="analysis-modules">
<h1>3. Analysis modules<a class="headerlink" href="#analysis-modules" title="Permalink to this headline">¶</a></h1>
<p>The <tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.analysis</span></tt> module contains code to carry out
specific analysis functionality. It is based on the core functionality
(i.e. trajectory I/O, selections etc). The analysis modules can be
used as examples for how to use MDAnalysis but also as working code
for research projects; typically all contributed code has been used by
the authors in their own work.</p>
<p>Please see the individual module documentation for additional
references and citation information.</p>
<p>These modules are not imported by default; in order to use them one
has to import them from <tt class="xref py py-mod docutils literal"><span class="pre">MDAnalysis.analysis</span></tt>, for instance</p>
<div class="highlight-python"><div class="highlight"><pre><span class="kn">import</span> <span class="nn">MDAnalysis.analysis.align</span>
</pre></div>
</div>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">Some of the modules require additional Python packages such as
<tt class="xref py py-mod docutils literal"><span class="pre">scipy</span></tt> from the <a class="reference external" href="http://www.scipy.org/">SciPy</a> package or <tt class="xref py py-mod docutils literal"><span class="pre">networkx</span></tt> from
<a class="reference external" href="http://networkx.lanl.gov/">NetworkX</a>. These package are <em>not automatically installed</em> (although
one can add the <tt class="docutils literal"><span class="pre">[analysis]</span></tt> requirement to the
<strong class="program">easy_install</strong> command line to force their installation.</p>
</div>
<p class="rubric">Contents</p>
<div class="toctree-wrapper compound">
<ul>
<li class="toctree-l1"><a class="reference internal" href="analysis/align.html">3.1. Coordinate fitting and alignment &#8212; <tt class="docutils literal"><span class="pre">MDAnalysis.analysis.align</span></tt></a></li>
<li class="toctree-l1"><a class="reference internal" href="analysis/contacts.html">3.2. Native contacts analysis &#8212; <tt class="docutils literal"><span class="pre">MDAnalysis.analysis.contacts</span></tt></a></li>
<li class="toctree-l1"><a class="reference internal" href="analysis/distances.html">3.3. Distance analysis &#8212; <tt class="docutils literal"><span class="pre">MDAnalysis.distances</span></tt></a></li>
<li class="toctree-l1"><a class="reference internal" href="analysis/density.html">3.4. Generating densities from trajectories &#8212; <tt class="docutils literal"><span class="pre">MDAnalysis.analysis.density</span></tt></a></li>
<li class="toctree-l1"><a class="reference internal" href="analysis/hbonds.html">3.5. Hydrogen Bond analysis &#8212; <tt class="docutils literal"><span class="pre">MDAnalysis.analysis.hbonds</span></tt></a></li>
<li class="toctree-l1"><a class="reference internal" href="analysis/helanal.html">3.6. HELANAL &#8212; analysis of protein helices</a></li>
<li class="toctree-l1"><a class="reference internal" href="analysis/leaflet.html">3.7. Leaflet identification &#8212; <tt class="docutils literal"><span class="pre">MDAnalysis.analysis.leaflet</span></tt></a></li>
</ul>
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